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UVM BIOC 205 - HOMEWORK II and Swiss-PDB Viewer Tutorial

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Student Name____________________________BIOCHEMISTRY IHOMEWORK IIandSwiss-PDB Viewer TutorialDUE 9/26/0362 points total1). 8 points totalT or F (2 points each; if false, briefly state why it is false)____ The pH at which a peptide has no net charge is its isoelectric point.____Hydrophilic side chains of amino acid residues normally locate themselves towardthe exterior of globular proteins.____Proteins are made up of D-amino acids..____ Mutations always affect biological activity of a protein.2) 12 points totalFill in the blank:The α-helix is an example of a _______ structural element. It is a helical structureformed by ______ _______ between groups in peptide bonds. In particular, the ___________ of the ith residues of an a-helix is bonded to the ______ _____ of the (i+4)thresidue. The result is α-helical structure that repeats every ______ residues. The_____ of the helix, or distance along the axis per turn, is _______ nm. Thearrangement orients the amide planes ______ to the helix axis and the side chains_____ to the helix axis.Student Name____________________________3). 3 pointsMyoglobin was the first globular protein whose structure was solved by x-raycrystallography. The sequence of helix E is given below. Using the helix wheel, map outthe amino acid side chains.E Helix Sequence: S E D L K H G A T V L T A L G G I LWhat is the nature of the α-helix? Where would it most likely be found?4). 3 pointsConsider what we know about amino acid structure. Briefly describe three factors aboutamino acids that do not foster α-helical formation. (I will give a bonus point fordescribing four factors).Student Name____________________________5). 7 points totalFor the sequence drawn below, write the one letter code and determine the pI. What isthe charge on this molecule at pH 12?Student Name____________________________6). 6 pointsDetermine the amino acid sequence of the following oligopeptide from the experimentaldata below.1. The amino acid composition is found to be [ala, lys, phe, met, cys, plussome decomposition products].2. The peptide has a molecular weight around 700 Da and absorbs at280 nm.3. Treatment with carboxypeptidase results in tryptophan and apeptide.4. CNBr treatment yields a tetrapeptide and a dipeptide.5. Trypsin digestion produces an amino acid and a pentapeptide with meton the amino end.6. Chymotrypsin digestion yields a dipeptide and a tetrapeptide.7). 4 points totalDetermine the subunit composition of a protein based on the following information. Beexplicit in describing the subunit composition.Molecular mass by gel chromatography: 200 kDMolecular mass by SDS-PAGE: 100 kDMolecular mass by SDS-PAGE with 2-ME present: 40 kD and 60 kDStudent Name____________________________Homework questions based PDB file and Swiss-PDB Viewer Tutorial (attached at end ofhomework).8). 17 points totalFrom the PDB file, answer the following questions.a). What is the chemical classification for carbonic anhydrase II and what does thisgeneral type of protein class do (from class notes)?b). What experimental method was used to determine the structure?c). What is the source of CA2?d). How many amino acid residues comprise this protien?e). What is (are) the main hetero-atoms?f). Were all amino acids detectable in the structure?g). How many W, Y, F respectively are in the structure? Would you expect this protein tohave an absorbance at 280 nm?h). How many α-helices, β-sheets and turns are defined in the structure? (Try to findthem in the structure using Swiss-PDB Viewer).i). How many water molecules are found in the structure?j). As a thought question, not related to the PDB file, would you think that many of thewaters are found on the inside of the structure? Why or why not?Student Name____________________________Question related to the Swiss-PDB tutorial.9). 2 pointsa). The Zinc hetero-atom in the structure of CA2 plays a role in catalysis. Described itslocation in the structure.b). What statements about the location of an enzyme's active site can be made based onthis information?Student Name____________________________Protein Data Bank and Swiss-PDB Viewer HomeworkThe ultimate goal behind this tutorial is to get familiar with working with Swiss-PDBViewer. An additional tutorial that is recommended by one of my colleagues who does x-ray crystallography (but which I haven't personally used) is located athttp://www.usm.maine.edu/~rhodes/SPVTut/index.html.Why Swiss-PDB Viewer? It appears to be the most used, and best supported structuralimaging software available. It is available free athttp://us.expasy.org/spdbv/mainpage.html. From that site you can download versions forMac, PC, Linux and SGI. To date, I have used a different program to view molecules(Rasmol), but it isn't as powerful as Swiss-PDB Viewer and it is no longer supported. Thisis a learning experience for me also.The best way to learn about any software is to "play" with it. Try out the differentmenus and see what happens. Don't be afraid to explore the program. This tutorial isbased on what I did to learn basic familiarization with the program. Answer thehomework questions as you go through this exercise.A). We will start with the Protein Data Bank located at http://www.rcsb.org/pdb/.Download the structure for carbonic anhydrase II. The pdf id is 1CA2.In the homework, there are a series of questions related to the pdb file.B). Open the structure with Swiss-PDB viewer.One homework question related to this section.Rotate the structure: You have a stick structure of the atoms in front of you.Color scheme: White - carbonBlue - nitrogenRed - oxygenYellow - sulfurCan you identify amino acids based on their chemical structure?Look for histidine, tyrosineWhat sulfur-containing amino acids does the structure contain?C). Manipulate the image:Under the "Display" menu:Show backbone oxygens: Turn off and on; see how the structure is altered.Student Name____________________________Play with other options to check them out; some options alter the image,some are not active right now.D). Control panel window:The control panel allows you to highlight and manipulate selected amino acidresidues. We are going to manipulate the image through the control panel. You have theoption of affecting individual amino acids by clicking in the appropriate column next tothe amino acid, selecting all amino acids by holding down the shift key and clicking at thetop of the column or selecting specific groups of amino


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UVM BIOC 205 - HOMEWORK II and Swiss-PDB Viewer Tutorial

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